Organism No. 1

History

A flashback revealed that it and its twin, Organism No. 2, were created from exposure to strange radiation when they were viruses floating in space. After being mutated, they attached themselves to a meteor, which crashed into the Hoenn region and was found by Professor Cozmo, who took it to the Mossdeep Space Center for study. However, during Courtney's attack on the Space Center, Team Rocket was able to steal the two space Pokémon in the confusion.

Organism No. 1 first makes an appearance as an invisible enemy on the Seagallop Ferry in which it attacked Green and easily defeated her Pokémon. It then kidnapped her parents by sucking them into a miniature black hole, causing Green to go into a coma from the shock of losing the parents she had wanted to meet for so long.

It was revealed later that Organism No. 1 was used to provoke Red, whose anger would alert Organism No. 2, who was connected to him, and lure it so it could be captured.

As Sird explained Organism No. 2's history, she mentioned that as they no longer had use for Organism No. 1, they "disposed of it". Whether this means Organism No. 1 is missing or no longer alive has yet to be revealed.

Trivia

Organism No. 1 was invisible, but still detectable by Green's Silph Scope thanks to an upgrade that extended its detection ability to include all invisible Pokémon.

A flashback revealed that it and its twin, Organism No. 1, were created from exposure to strange radiation when they were viruses floating in space. After being mutated, they attached themselves to a meteor, which crashed into the Hoenn region and was found by Professor Cozmo, who took it to the Mossdeep Space Center for study. However, during Courtney's attack on the Space Center, Team Rocket was able to steal the two space Pokémon in the confusion.

Organism No. 2 eventually broke free from captivity and escaped from Team Rocket. In the process, it was able to absorb Red's blood, causing a connection to form between them and leading him to believe that he was its ancestor.

Organism No. 2 first makes its appearance on Three Island, where it saved Lostelle from a biker gang, though its intentions for doing so are unknown; its name is revealed here by Giovanni.

On Four Island, the Kanto Pokédex holders are used to bait the Deoxys out of hiding. After confronting Carr, Red battles with the mysterious creature, though he is soundly defeated, breaking Red's spirit for battling. However, the battle left it injured, so it retreats to Birth Island for recovery. This is cut short when Giovanni arrives and captures it, as it is too exhausted to fight back.

Giovanni and Organism No. 2

On the Team Rocket airship, Giovanni uses Deoxys to battle Red, who joined forces with Mewtwo. After a long and tough battle, Red and Mewtwo emerge victorious. Yellow also arrives on the airship, and her powers allow her to hear Deoxys's thoughts while its origins are explained by Sird. When Carr hijacks the airship, Red helps the weakened Deoxys and asks it to use its power to create black holes and send Silver, Giovanni, Yellow, and Mewtwo to safety.

After the four is sent to safety, Organism No. 2 helps Red to locate explodingForretress hidden by Carr to blow up the airship. They dispatch all ten with ease and land the airship safely, and Deoxys thanks Red and sets off to find its comrade, Organism No. 1, and find a region with special meteors that allow them to freely change between form. When it leaves, Sird is revealed to be alive after being thrown off the airship, and attempts to capture it. Red, with Yellow in his arms, Blue, Green, Silver, and Mewtwo jump in the way of Sird's attack to protect it, and all of them, except Mewtwo, are turned to stone as a result.